Bioimaging is being used increasingly in endocrinology-based research projects, and instrumentation is available at most universities and through national infrastructures such as Danish Bioimaging. Even though these technologies are at your fingertips, how do you know which instrument to choose? How to generate high quality quantitative data? What methods should you choose for analysing the data? 

This course helps answer those questions and gives you the confidence and inspiration to apply bioimaging to answer your specific research questions. 

In interactive lectures, you will learn how to design a bioimaging pipeline for addressing your specific research question starting from choice of the right instrument and extending to image analysis and publication. Through inspirational talks by leading scientists in exploratory biomedical research, corporate preclinical development, and AI-based image analysis, you will be exposed to different bioimaging modalities and see examples of their application. 

Microscopy demo workshops with some possibility for hands-on operation include: Spinning disk microscopy (Andor’s BC43) and confocal laser scanning microscopy (Olympus FV1200). During these workshops we will demonstrate how to  set up an instrument for getting results which are suitable for quantitative analysis.

The data analysis workshops are taught by specialists from the Danish Bioimaging Image analysis core facility and Andor (Imaris). They will introduce the open-source image analysis software ImageJ/Fiji and the commercial software Imaris. You will learn how to set up your own analysis pipeline including preprocessing, rendering, segmenting and quantifying images and writing macros. You will also be introduced to machine learning for image analysis. If you already have your own 3D imaging data you will be able to get started on analysing it with input from the course instructors. 

In this intensive residential course we have also set time aside for networking with the other course participants and teachers during poster sessions and dinners, allowing you to develop working relationships over common interests in research and bioimaging technology. 

Briefly, the programme consists of:

Day 1: 

Introduction to 3D quantitative imaging 

Poster sessions

Inspirational scientific talk on imaging application

Dinner and networking

Day2: 

Two microscopy demo workshops 

Inspirational scientific talk on imaging application

Day 3:

Talk on European, nordic, and danish imaging infrastructure 

ImageJ image analysis workshop

Day 4:

ImageJ image analysis workshop continued

Group work on own data and presentations

Scientific talk on AI assisted image analysis

Dinner and networking

Day 5:

Imaris image analysis workshop

Talk on how to publish 3D image data 

To complete the course you are expected to:

• Read the material provided
• Complete an image analysis tutorial and hand-in 
• Prepare a project poster
• Actively attend all 5 days
• Participate in oral presentations of image analysis results

After the course, you will be able to: 

1. Develop a bioimaging pipeline for your specific scientific question, including choosing the right instrument, acquiring the images, and analysing the images
2. Be able to perform a quantitative analysis of your images
3. Increase your confidence in working with bioimaging
4. Be inspired to use bioimaging
5. Know what instrumentation is available in Danish Bioimaging Infrastructure
6. Have a network of other students and researchers within bioimaging 

Speakers:

Aisha Sivakumar, Applications Specialist, Andor Technology (UK)

Bernd Pulverer, Chief Editor, EMBO Reports

Jacob Hecksher-Sørensen, Director of Scientific Sales and Imaging Innovation, Gubra

Jakub Sedzinski,  Associate Professor at Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen

Jon Sporring, Professor at Department of Computer Science, University of Copenhagen

Julia Schweizer, Imaris Specialist and Regional Sales Engineer at Imaris, an Oxford Instruments brand

Ruediger Bader, Confocal Microscopy Specialist and Sales Team Leader at Andor, an Oxford Instruments brand 

Richard De Mets, Bioimage Analyst at Core Facility for Integrated Microscopy, University of Copenhagen

Tricia Loo, Bioimage Analyst, Danish Bioimaging Infrastructure Image Analysis Core Facility (DK)

Organisers:

Louise Dalgaard, Professor, Roskilde University (DK)

Pia Nyeng, Associate Professor, Roskilde University (DK)

Sebastian Tosi, Bioimage Analyst, Danish Bioimaging Infrastructure Image Analysis Core Facility (DK) (https://www.dbi-infra.eu/iacf/#Infrastructure)

In collaboration with Andor, An Oxford Instruments Company

The course is designed for PhD students interested in or already using 3D imaging and quantitative analysis of bioimages in their research projects. While PhD students will be prioritised researchers at all other levels are also welcome to apply. 

Prerequisites: 

Basic knowledge of biomedical sciences at a level corresponding to Danish university graduates in biology, molecular biology, biochemistry, biotechnology, molecular medicine, veterinary medicine, environmental sciences, nutrition, dentistry and similar fields in life and health sciences. 

Previous experience with basic fluorescence microscopy and/or image analysis.

Participants are selected based on abstract submission. Those with the most relevant and immediate need for training in bioimaging will be prioritised. Please submit your abstract along with your registration.

Please note that you are not guaranteed a seat on the course if you do not meet the target group requirements. Priority is given to participants employed at Danish research and health institutions or life science industry. If the event is overbooked, the DDEA reserves its right to select participants based on the defined requirements and country of employment.

What to bring:

• Your own laptop  with ImageJ/Fiji installed (installation instructions will be provided in the tutorial)
• Your own image dataset (if available)

Dinner registration 

The DDEA organises informal networking dinners on January 15 and 18. Participation in the dinner is free of charge and optional, but encouraged. Please sign up for the dinner upon registration, and indicate whether you have any dietary requirements.

Accommodation 

The DDEA offers accommodation in Roskilde for all participants who need it. Please note that we start the program at 8.30 and end at 17.00 most days.

Please sign up for accommodation, if needed, when you register for the event.

You will be informed about your overnight accommodation by the DDEA after the registration deadline.

Certification
A course certificate will be sent to all participants upon request at the end of the course. Full participation is required to attain 4 ECTS points. .

Latest cancellation date & no-show fee
Please note that it is free of charge to participate in the event, however the DDEA will charge a no-show fee of 1000 DKK if you do not show up and have not unregistered from the event by 7 January 2024 except in the case of illness or emergency.

Deadline for submission of abstracts:  17 December 2023

Abstract guidelines:
The abstract should be focused on your own project and how you will incorporate bioimaging methods. Be sure your abstract contains the following information and adheres to the following formatting guidelines before submission:

You may download the template here

The abstract should be max 1500 characters incl. spaces and written in Arial 10.

• Title of abstract (Use a short and specific title with title-style capitalization and put it in bold)

• Presenting author name(s) (Underline the presenting author’s name)

• Affiliation (Include unit, institution/company/hospital, city and country for all authors and put it in italic)

The body of the abstract contains the following content:

• Background and aim (including how bioimaging is incorporated in the project)
  Text in Arial 10

• Material and methods (including bioimaging methods)
  Text in Arial 10

• Results (if obtained to-date)
  Text in Arial 10

• Conclusion (and perspectives)
  Text in Arial 10

No images, figures, charts or tables should be included in the abstract.

Please proofread carefully before submission and submit a word file and please name the file that you submit with your name.

Poster guidelines:

Format  of poster: A0 or A1 – width max. 1 m/height max. 1.25 m (“Portrait format” is preferred due to the orientation of poster boards and space). The poster can be printed on regular paper(s) if you do not have access to a poster printing service.

Content of poster: The poster should be focused on your own project and how you will incorporate bioimaging methods. The poster should include the same content as outlined above for abstract, but may in addition contain images, figures, charts and  tables.